Updated from which previous version? Spot or process colors?
Our previous version was InDesign CC (64 bit). We use process colours, however on one instance, one of the colours in question was a spot colour.
We know of no such behavior.
Are you using the exact same PDF export presents for InDesign 10 and you used for InDesign 9?
What happens when you check the colors in Acrobat yourself? Are they the same as exported with the previous version?
One area that could make a difference in what your users see as color values would be if you previously used High Quality Print but now use PDF/X-4 as the PDF export settings due to the output intent profile of PDF/X-4 and how Acrobat displays colors.
Something I would try would be to produce a very simple InDesign-exported PDF with a few patches in well-defined, known colors, CMYK, RGB, and LAB, with both InDesign 9 and 10 and see whether measuring the colors in Acrobat shows any difference in output CMYK values or not for each of the patches.
If you are using custom color for your CMYK settings make sure that you set the right profile color in your InDesign CC 2014, since InDesign CC 2014 default color settings is set to "Working CMYK - U.S. Web Coated (SWOP) v2". InDesign CC 2014 then exports your file to PDF using the default profile.
In Previous InDesign CC the default values for Assign Profiles is set to Discard (use current working space) for RGB Profile and Discard (use current working space) for CMYK. But in InDesign CC 2013 if you are going to export an InDesign file into PDF, it will automatically use your Color Settings options for CMYK values. But in InDesign 2014 those settings will be ignored by InDesign because it will use the current Assigned Profile by InDesign. If you are going to check your your working space back in InDesign CC 2013 it was set to your CMYK Color Settings.
And Finally always check you pdf setting under Export PDF settings dialog box to No Color Conversion.
Hope this help. And I can't be sure if this will solve your problem. But at least I was trying to help.